RetrogeneDB ID:

retro_pabe_1129

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:14:71292497..71293220(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SAP25
Ensembl ID:ENSPPYG00000017415
Aliases:None
Description:Sin3A-associated protein, 25kDa [Source:HGNC Symbol;Acc:41908]


Retrocopy-Parental alignment summary:






>retro_pabe_1129
GGGCAAGGACCAAGGGGCGAGCCCTGGAGCTCTGGAGCGGACGCCCCCAGGGAGCTGGGGTCACCCCCATGGGACAGCCC
TTCCTAGACCCGGAGAGAGCAGCTGCTGCTGCCCCACCACCCACCAGGCCCGGCCACTGAGCAGCGCCCCGGAGCCCCAG
ATCCTCGTTCCCCCCAGGTGGCCTGGGAGGTGGCCCCCTCGAGGATGACTCCACTAGCGCCCTGGGACCCCAAGTACGAA
GCCAAAGCAGGACCTTGGCTGGTGTGGGGGGCCAACTGTAGCTCAGGAGCCTCGTTCTGAGGCCGGACGCTGTGTCACCC
CTCGTTCTGGCCGCTGTACGAGGCAGCCTCGGGCAGGGGTCTCAGGCCCGTGGCCCCTGCCACAGGGCATTGTAATGGAC
AGCAGGCGCCCCCGGATGCAGGGTTCCCGGTGATGTGCTATGAAGACGTCTTCCTCTCGGATCCTCTGCTGCCCCGGGGG
CAGCGTGTCCCCCTATACCTGTCCAAGGCCCCCCAGCAGATGATGGGCTCCCTGAAACTGCTGCCGCCGCCCCCCATCAT
GTCTGCCAAGGTTCTCCCCCGCCTGTCACCCTCCCGGGGCCCCTCCACTGCCTGGCTCAGCGGGCCGGAGCTGATCGCTC
TCACTGGCCTGCTGCAGGTGAGCCAGGGGGAGCCTAGGCCCAGCTCCTCCGCAGCTGGCCCCCCAGACCCTACCTCTGAC
CCA

ORF - retro_pabe_1129 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.71 %
Parental protein coverage: 50.63 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGEGAWGRCGCSLSPCPSS-PQPPSRSPSWTRREQLLLPHHPPGPATEQPPGAPDPRSPQVAWEVVPSRIT
G.G..G....S....P.....PP..SPS.TRREQLLLPHHPPGPATEQ.PGAPDPRSPQVAWEV.PSR.T
RetrocopyGQGPRGEPWSSGADAPRELGSPPWDSPS*TRREQLLLPHHPPGPATEQRPGAPDPRSPQVAWEVAPSRMT
ParentalPLAPWDPKYEVKAGPRPVWGANCSSGASFSGRTLCHPSFWPLYEAASGRGLRPVAPATGHWNGQQAPPDA
PLAPWDPKYE.KAGP..VWGANCSSGASF.GRTLCHPSFWPLYEAASGRGLRPVAPATGH.NGQQAPPDA
RetrocopyPLAPWDPKYEAKAGPWLVWGANCSSGASF*GRTLCHPSFWPLYEAASGRGLRPVAPATGHCNGQQAPPDA
ParentalGFPVMCCEDIFLSDPLLPRGQRVPLYLSKAPQQVRPSLQPSSPFPCSKPGLLHPPSPSKGPRFLAPLPFP
GFPVMC.ED.FLSDPLLPRGQRVPLYLSKAPQQ...SL....P.P......L...SPS.GP.........
RetrocopyGFPVMCYEDVFLSDPLLPRGQRVPLYLSKAPQQMMGSLKLLPPPPIMSAKVLPRLSPSRGPSTAWLSGPE
ParentalLSRYPGLLRLSQTHPRPSTSPLPPPQESQMP
L....GLL..SQ..PRPS.S...PP.....P
RetrocopyLIALTGLLQVSQGEPRPSSSAAGPPDPTSDP

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .06 RPM 2 .32 RPM
SRP007412_cerebellum 0 .00 RPM 2 .68 RPM
SRP007412_heart 0 .00 RPM 0 .51 RPM
SRP007412_kidney 0 .03 RPM 4 .67 RPM
SRP007412_liver 0 .03 RPM 2 .91 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1129 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1129 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1129 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000152731 retrocopy
Homo sapiens ENSG000002053071 retrocopy
Gorilla gorilla ENSGGOG000000137081 retrocopy
Pongo abelii ENSPPYG00000017415 1 retrocopy
retro_pabe_1129 ,
Pan troglodytes ENSPTRG000000194951 retrocopy



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